diff --git a/_config.yml b/_config.yml index 8c630f463..3f9121eba 100644 --- a/_config.yml +++ b/_config.yml @@ -7,20 +7,227 @@ imgurl: /images author: name: OBO Technical WG ontologies: -- contact: {email: David Blackburn, label: david.c.blackburn@gmail.com} - homepage: http://github.com/seger/aao - id: aao - is_obsolete: true +- alternatePrefix: ChEBI + browsers: + - {label: CHEBI, title: EBI CHEBI Browser, url: 'http://www.ebi.ac.uk/chebi/chebiOntology.do?treeView=true&chebiId=CHEBI:24431#graphView'} + build: {infallible: 1, method: archive, path: archive/main, source_url: 'http://build.berkeleybop.org/job/build-chebi/lastSuccessfulBuild/artifact/*zip*/archive.zip'} + contact: {email: gowen@ebi.ac.uk, label: Gareth Owen} + description: A structured classification of molecular entities of biological interest + focusing on 'small' chemical compounds. + domain: biochemistry + homepage: http://www.ebi.ac.uk/chebi + id: chebi + in_foundry_order: 1 layout: ontology_detail - replaced_by: uberon - taxon: {id: 'NCBITaxon:8292', label: Amphibia} - title: Amphibian gross anatomy -- contact: {email: Animal Diversity Web technical staff, label: adw_geeks@umich.edu} - homepage: http://www.animaldiversity.org - id: adw - is_obsolete: true + ontology_purl: http://purl.obolibrary.org/obo/chebi.owl + page: http://www.ebi.ac.uk/chebi/init.do?toolBarForward=userManual + products: + - {id: chebi.owl, ontology_purl: 'http://purl.obolibrary.org/obo/chebi.owl'} + - {id: chebi.obo, ontology_purl: 'http://purl.obolibrary.org/obo/chebi.obo'} + title: Chemical Entities of Biological Interest + tracker: https://sourceforge.net/p/chebi/curator-requests/ + twitter: chebit +- browsers: + - {label: DO, title: DO Browser, url: 'http://www.disease-ontology.org/'} + build: {infallible: 1, method: obo2owl, source_url: 'http://sourceforge.net/p/diseaseontology/code/HEAD/tree/trunk/HumanDO.obo?format=raw'} + contact: {email: lynn.schriml@gmail.com, label: Lynn Schriml} + description: An ontology for describing the classification of human diseases organized + by etiology. + domain: disease + facebook: https://www.facebook.com/diseaseontology + homepage: http://diseaseontology.sourceforge.net/ + id: doid + in_foundry_order: 1 layout: ontology_detail - title: Animal natural history and life history + license: {label: CC-BY, logo: 'http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png', + url: 'http://creativecommons.org/licenses/by/3.0/'} + ontology_purl: http://purl.obolibrary.org/obo/doid.owl + page: http://diseaseontology.sourceforge.net/ + products: + - {id: doid.owl, ontology_purl: 'http://purl.obolibrary.org/obo/doid.owl'} + - {id: doid.obo, ontology_purl: 'http://purl.obolibrary.org/obo/doid.obo'} + publications: + - {id: 'http://www.ncbi.nlm.nih.gov/pubmed/?term=25348409', title: 'Disease Ontology + 2015 update: an expanded and updated database of human diseases for linking + biomedical knowledge through disease data'} + taxon: {id: 'NCBITaxon:9606', label: Homo sapiens} + title: Human Disease Ontology + tracker: http://sourceforge.net/tracker/?func=add&group_id=79168&atid=555739 + twitter: diseaseontology +- browsers: + - {label: AmiGO, title: Gene Ontology AmiGO 2 Browser, url: 'http://amigo.geneontology.org/amigo/term/GO:0008150#display-lineage-tab'} + build: {checkout: 'svn --ignore-externals co svn://ext.geneontology.org/trunk/ontology', + infallible: 1, method: vcs, system: svn} + dependencies: + - {id: uberon, subset: go/extensions/uberon_import.owl} + - {id: cl, subset: go/extensions/cl_import.owl} + - {id: ncbitaxon, subset: go/extensions/ncbitaxon_import.owl} + - {id: ro, subset: go/extensions/ro_import.owl} + - connects: + - {id: nifstd} + - {id: go} + description: Bridging axioms between nifstd and go + id: go/extensions/go-bridge-to-nifstd.owl + publications: + - {id: 'http://www.ncbi.nlm.nih.gov/pubmed/24093723', title: 'The Gene Ontology + (GO) Cellular Component Ontology: integration with SAO (Subcellular Anatomy + Ontology) and other recent developments.'} + title: GO bridge to NIFSTD + type: BridgeOntology + depicted_by: http://geneontology.org/sites/default/files/go-logo-icon.mini__0.png + description: An ontology for describing the function of genes and gene products + domain: biology + facebook: https://www.facebook.com/Gene-Ontology-305908656519/ + id: go + in_foundry_order: 1 + integration_server: http://build.berkeleybop.org/view/GO + label: GO + layout: ontology_detail + license: {label: CC-BY, logo: 'http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png', + url: 'http://creativecommons.org/licenses/by/3.0/'} + ontology_purl: http://purl.obolibrary.org/obo/go.owl + products: + - {id: go.owl, ontology_purl: 'http://purl.obolibrary.org/obo/go.owl'} + - {description: The core ontology plus axioms connecting to select external ontologies, + id: go/extensions/go-plus.owl, ontology_purl: 'http://purl.obolibrary.org/obo/go/extensions/go-plus.owl', + title: GO-Plus} + - {description: Classes added to ncbitaxon for groupings such as prokaryotes, id: go/extensions/go-taxon-groupings.owl, + ontology_purl: 'http://purl.obolibrary.org/obo/go/extensions/go-taxon-groupings.owl', + title: GO Taxon Groupings} + taxon: {id: 'NCBITaxon:1', label: All life} + termgenie: http://go.termgenie.org + title: Gene Ontology + tracker: https://github.com/geneontology/go-ontology/issues/ + twitter: news4go +- browsers: + - {label: BioPortal, title: BioPortal Browser, url: 'http://bioportal.bioontology.org/ontologies/OBI?p=classes'} + build: {source_url: 'http://purl.obofoundry.org/obo/obi/repository/trunk/src/ontology/branches/'} + contact: {email: bpeters@liai.org, label: Bjoern Peters} + depicted_by: https://svn.code.sf.net/p/obi/code/trunk/web/htdocs/images/obi-lotext.png + description: An integrated ontology for the description of life-science and clinical + investigations + domain: experiments + homepage: http://obi-ontology.org + id: obi + in_foundry_order: 1 + integration_server: http://build.berkeleybop.org/job/build-obi/ + layout: ontology_detail + license: {label: CC-BY, logo: 'http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png', + url: 'http://creativecommons.org/licenses/by/3.0/'} + mailing_list: http://groups.google.com/group/obi-users + ontology_purl: http://purl.obolibrary.org/obo/obi.owl + products: + - {id: obi.owl, ontology_purl: 'http://purl.obolibrary.org/obo/obi.owl', title: OBI} + - {id: obi/obi_core.owl, ontology_purl: 'http://purl.obolibrary.org/obo/obi/obi_core.owl', + title: OBI Core} + title: Ontology for Biomedical Investigations + tracker: http://purl.obofoundry.org/obo/obi/tracker +- browsers: + - {label: Aber-OWL, title: Aber-OWL Ontology Browser, url: 'http://aber-owl.net/ontology/PATO'} + - {label: BioPortal, title: BioPortal Ontology Browser, url: 'https://bioportal.bioontology.org/ontologies/PATO'} + - {label: OntoBee, title: OntoBee Browser, url: 'http://www.ontobee.org/browser/index.php?o=PATO'} + build: {infallible: 1, method: obo2owl, source_url: 'https://raw.githubusercontent.com/pato-ontology/pato/master/pato.obo'} + contact: {email: g.gkoutos@gmail.com, label: George Gkoutos} + description: An ontology of phenotypic qualities (properties, attributes or characteristics) + domain: phenotype + homepage: https://github.com/pato-ontology/pato/ + id: pato + in_foundry_order: 1 + jobs: + - {id: 'http://build.berkeleybop.org/job/build-pato', type: DryRunBuild} + layout: ontology_detail + license: {label: CC-BY, logo: 'http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png', + url: 'http://creativecommons.org/licenses/by/3.0/'} + ontology_purl: http://purl.obolibrary.org/obo/pato.owl + products: + - {id: pato.owl, ontology_purl: 'http://purl.obolibrary.org/obo/pato.owl'} + - {id: pato.obo, ontology_purl: 'http://purl.obolibrary.org/obo/pato.obo'} + repository: https://github.com/pato-ontology/pato/ + title: Phenotypic quality + tracker: https://github.com/pato-ontology/pato/issues +- build: {infallible: 1, method: obo2owl, notes: switch to vcs method, source_url: 'https://raw.githubusercontent.com/Planteome/plant-ontology/master/po-release-files/plant_ontology.obo'} + contact: {email: jaiswalp@science.oregonstate.edu, label: Pankaj Jaiswal} + description: The Plant Ontology is a structured vocabulary and database resource + that links plant anatomy, morphology and growth and development to plant genomics + data. + domain: anatomy and development + homepage: http://www.plantontology.org + id: po + in_foundry_order: 1 + layout: ontology_detail + license: {label: CC-BY, logo: 'http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png', + url: 'http://creativecommons.org/licenses/by/3.0/'} + ontology_purl: http://purl.obolibrary.org/obo/po.owl + page: http://www.plantontology.org/amigo/go.cgi + products: + - {id: po.owl, ontology_purl: 'http://purl.obolibrary.org/obo/po.owl'} + - {id: po.obo, ontology_purl: 'http://purl.obolibrary.org/obo/po.obo'} + publications: + - {id: 'http://www.ncbi.nlm.nih.gov/pubmed/23220694', title: The plant ontology + as a tool for comparative plant anatomy and genomic analyses.} + - {id: 'http://www.ncbi.nlm.nih.gov/pubmed/22847540', title: Ontologies as integrative + tools for plant science.} + taxon: {id: 'NCBITaxon:33090', label: Viridiplantae} + title: Plant Ontology + tracker: https://github.com/Planteome/plant-ontology/issues + twitter: planteome +- build: {infallible: 0, method: obo2owl, oort_args: --no-reasoner, source_url: 'ftp://ftp.pir.georgetown.edu/databases/ontology/pro_obo/pro.obo'} + contact: {email: dan5@georgetown.edu, label: Darren Natale} + description: an ontological representation of protein-related entities + development: {id_policy: 'https://pir17.georgetown.edu/confluence/display/PROWIKI/PRO+URI+policy'} + documentation: ftp://ftp.pir.georgetown.edu/databases/ontology/pro_obo/pro_readme.txt + domain: proteins + homepage: http://proconsortium.org + id: pr + in_foundry_order: 1 + layout: ontology_detail + ontology_purl: http://purl.obolibrary.org/obo/pr.owl + products: + - {id: pr.owl, ontology_purl: 'http://purl.obolibrary.org/obo/pr.owl'} + title: PRotein Ontology (PRO) + tracker: http://sourceforge.net/tracker/?group_id=266825&atid=1135711 +- build: {infallible: 0, method: obo2owl, source_url: 'https://raw.githubusercontent.com/xenopus-anatomy/xao/master/xenopus_anatomy.obo'} + description: Anatomy and development of the African clawed frog (Xenopus laevis). + domain: anatomy + homepage: http://www.xenbase.org/anatomy/xao.do?method=display + id: xao + in_foundry_order: 1 + layout: ontology_detail + license: {label: CC-BY, logo: 'http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png', + url: 'http://creativecommons.org/licenses/by/3.0/'} + ontology_purl: http://purl.obolibrary.org/obo/xao.owl + products: + - {id: xao.owl, ontology_purl: 'http://purl.obolibrary.org/obo/xao.owl'} + publications: + - {id: 'http://www.ncbi.nlm.nih.gov/pubmed/18817563', title: An ontology for Xenopus + anatomy and development.} + - {id: 'http://www.ncbi.nlm.nih.gov/pubmed/24139024', title: 'Enhanced XAO: the + ontology of Xenopus anatomy and development underpins more accurate annotation + of gene expression and queries on Xenbase.'} + taxon: {id: 'NCBITaxon:8353', label: Xenopus} + title: Xenopus anatomy and development + tracker: https://github.com/xenopus-anatomy/xao/issues +- build: {infallible: 1, method: obo2owl, notes: may be ready to switch to vcs soon, + source_url: 'https://raw.githubusercontent.com/cerivs/zebrafish-anatomical-ontology/master/src/zebrafish_anatomy.obo'} + contact: {email: zfinadmin@zfin.org, label: ZFIN administrators} + description: A structured controlled vocabulary of the anatomy and development of + the Zebrafish + domain: anatomy + homepage: http://zfin.org/zf_info/anatomy/dict/sum.html + id: zfa + in_foundry_order: 1 + layout: ontology_detail + license: {label: CC-BY, logo: 'http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png', + url: 'http://creativecommons.org/licenses/by/3.0/'} + ontology_purl: http://purl.obolibrary.org/obo/zfa.owl + products: + - {id: zfa.owl, ontology_purl: 'http://purl.obolibrary.org/obo/zfa.owl'} + publications: + - {id: 'http://www.ncbi.nlm.nih.gov/pubmed/24568621', title: 'The zebrafish anatomy + and stage ontologies: representing the anatomy and development of Danio rerio.'} + taxon: {id: 'NCBITaxon:7954', label: Danio} + title: Zebrafish anatomy and development + tracker: https://github.com/cerivs/zebrafish-anatomical-ontology/issues - build: {checkout: 'git clone https://github.com/obophenotype/human-developmental-anatomy-ontology.git', method: vcs, path: src/ontology, system: git} contact: {email: J.Bard@ed.ac.uk, label: Jonathan Bard} @@ -62,13 +269,6 @@ ontologies: - {id: apo.owl, ontology_purl: 'http://purl.obolibrary.org/obo/apo.owl'} taxon: {id: 'NCBITaxon:4890', label: Ascomycota} title: Ascomycete phenotype ontology -- contact: {email: David Blackburn, label: david.c.blackburn@gmail.com} - homepage: http://www.amphibanat.org - id: ato - is_obsolete: true - layout: ontology_detail - taxon: {id: 'NCBITaxon:8292', label: Amphibia} - title: Amphibian taxonomy - contact: {email: jiezheng@upenn.edu, label: Jie Zheng} description: An application ontology built for beta cell genomics studies. homepage: https://github.com/obi-bcgo/bcgo @@ -113,37 +313,18 @@ ontologies: - {id: bfo.obo, ontology_purl: 'http://purl.obolibrary.org/obo/bfo.obo'} title: Basic Formal Ontology tracker: https://github.com/BFO-ontology/BFO/issues -- build: {method: obo2owl, source_url: 'http://4dx.embl.de/4DXpress_4d/edocs/bilateria_mrca.obo'} - contact: {email: henrich@embl.de, label: Thorsten Heinrich} +- build: {checkout: 'git clone https://github.com/obophenotype/biological-spatial-ontology.git', + infallible: 1, method: vcs, path: src/ontology, system: git} + contact: {email: cjmungall@lbl.gov, label: Chris Mungall} + description: An ontology for respresenting spatial concepts, anatomical axes, gradients, + regions, planes, sides, and surfaces domain: anatomy - homepage: http://4dx.embl.de/4DXpress - id: bila - is_obsolete: true + homepage: https://github.com/obophenotype/biological-spatial-ontology + id: bspo layout: ontology_detail - products: - - {id: bila.owl, ontology_purl: 'http://purl.obolibrary.org/obo/bila.owl'} - replaced_by: uberon - taxon: {id: 'NCBITaxon:33213', label: Bilateria} - title: Bilateria anatomy -- contact: {email: Vivian Lee, label: vlee@ebi.ac.uk} - homepage: http://www.ebi.ac.uk/Rebholz-srv/GRO/GRO.html - id: bootstrep - is_obsolete: true - layout: ontology_detail - replaced_by: molecular_function - title: Gene Regulation Ontology -- build: {checkout: 'git clone https://github.com/obophenotype/biological-spatial-ontology.git', - infallible: 1, method: vcs, path: src/ontology, system: git} - contact: {email: cjmungall@lbl.gov, label: Chris Mungall} - description: An ontology for respresenting spatial concepts, anatomical axes, gradients, - regions, planes, sides, and surfaces - domain: anatomy - homepage: https://github.com/obophenotype/biological-spatial-ontology - id: bspo - layout: ontology_detail - license: {label: CC-BY, logo: 'http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png', - url: 'http://creativecommons.org/licenses/by/3.0/'} - ontology_purl: http://purl.obolibrary.org/obo/bspo.owl + license: {label: CC-BY, logo: 'http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png', + url: 'http://creativecommons.org/licenses/by/3.0/'} + ontology_purl: http://purl.obolibrary.org/obo/bspo.owl products: - {id: bspo.owl, ontology_purl: 'http://purl.obolibrary.org/obo/bspo.owl'} publications: @@ -210,26 +391,6 @@ ontologies: taxon: {id: 'NCBITaxon:6605', label: Cephalopod} title: Cephalopod Ontology tracker: https://github.com/obophenotype/cephalopod-ontology/issues -- alternatePrefix: ChEBI - browsers: - - {label: CHEBI, title: EBI CHEBI Browser, url: 'http://www.ebi.ac.uk/chebi/chebiOntology.do?treeView=true&chebiId=CHEBI:24431#graphView'} - build: {infallible: 1, method: archive, path: archive/main, source_url: 'http://build.berkeleybop.org/job/build-chebi/lastSuccessfulBuild/artifact/*zip*/archive.zip'} - contact: {email: gowen@ebi.ac.uk, label: Gareth Owen} - description: A structured classification of molecular entities of biological interest - focusing on 'small' chemical compounds. - domain: biochemistry - homepage: http://www.ebi.ac.uk/chebi - id: chebi - in_foundry_order: 1 - layout: ontology_detail - ontology_purl: http://purl.obolibrary.org/obo/chebi.owl - page: http://www.ebi.ac.uk/chebi/init.do?toolBarForward=userManual - products: - - {id: chebi.owl, ontology_purl: 'http://purl.obolibrary.org/obo/chebi.owl'} - - {id: chebi.obo, ontology_purl: 'http://purl.obolibrary.org/obo/chebi.obo'} - title: Chemical Entities of Biological Interest - tracker: https://sourceforge.net/p/chebi/curator-requests/ - twitter: chebit - build: {method: owl2obo, source_url: 'http://semanticchemistry.googlecode.com/svn/trunk/ontology/cheminf.owl'} contact: {email: hastings@ebi.ac.uk, label: Janna Hastings} description: Includes terms for the descriptors commonly used in cheminformatics @@ -367,14 +528,6 @@ ontologies: - {id: cvdo.owl, ontology_purl: 'http://purl.obolibrary.org/obo/cvdo.owl'} title: Cardiovascular Disease Ontology tracker: https://code.google.com/p/cvdo/issues/list -- contact: {email: Lindsay Cowell, label: Lindsay.Cowell@utsouthwestern.edu} - homepage: http://www.dukeontologygroup.org/Projects.html - id: dc_cl - is_obsolete: true - layout: ontology_detail - replaced_by: cl - taxon: {id: all, label: null} - title: Dendritic cell - build: {method: obo2owl, source_url: 'https://raw.githubusercontent.com/dictyBase/migration-data/master/ontologies/dicty_anatomy.obo'} contact: {email: r-chisholm@northwestern.edu, label: Rex Chisholm} description: A structured controlled vocabulary of the anatomy of the slime-mould @@ -423,33 +576,6 @@ ontologies: products: - {id: dinto.owl, ontology_purl: 'http://purl.obolibrary.org/obo/dinto.owl'} title: The Drug-drug Interaction Ontology -- browsers: - - {label: DO, title: DO Browser, url: 'http://www.disease-ontology.org/'} - build: {infallible: 1, method: obo2owl, source_url: 'http://sourceforge.net/p/diseaseontology/code/HEAD/tree/trunk/HumanDO.obo?format=raw'} - contact: {email: lynn.schriml@gmail.com, label: Lynn Schriml} - description: An ontology for describing the classification of human diseases organized - by etiology. - domain: disease - facebook: https://www.facebook.com/diseaseontology - homepage: http://diseaseontology.sourceforge.net/ - id: doid - in_foundry_order: 1 - layout: ontology_detail - license: {label: CC-BY, logo: 'http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png', - url: 'http://creativecommons.org/licenses/by/3.0/'} - ontology_purl: http://purl.obolibrary.org/obo/doid.owl - page: http://diseaseontology.sourceforge.net/ - products: - - {id: doid.owl, ontology_purl: 'http://purl.obolibrary.org/obo/doid.owl'} - - {id: doid.obo, ontology_purl: 'http://purl.obolibrary.org/obo/doid.obo'} - publications: - - {id: 'http://www.ncbi.nlm.nih.gov/pubmed/?term=25348409', title: 'Disease Ontology - 2015 update: an expanded and updated database of human diseases for linking - biomedical knowledge through disease data'} - taxon: {id: 'NCBITaxon:9606', label: Homo sapiens} - title: Human Disease Ontology - tracker: http://sourceforge.net/tracker/?func=add&group_id=79168&atid=555739 - twitter: diseaseontology - browsers: - {label: FB, title: FlyBase Browser, url: 'http://flybase.org/.bin/cvreport.html?cvterm=FBcv:0000347'} build: {infallible: 0, method: owl2obo, source_url: 'http://purl.obolibrary.org/obo/fbcv/dpo.owl'} @@ -500,22 +626,6 @@ ontologies: of scientific evidence using the Evidence Ontology (ECO)} title: Evidence ontology tracker: https://github.com/evidenceontology/evidenceontology/issues -- contact: {email: Jonathan Bard, label: J.Bard@ed.ac.uk} - homepage: http://genex.hgu.mrc.ac.uk/ - id: ehda - is_obsolete: true - layout: ontology_detail - replaced_by: ehdaa2 - taxon: {id: 'NCBITaxon:9606', label: Homo sapiens} - title: Human developmental anatomy, timed version -- contact: {email: Jonathan Bard, label: J.Bard@ed.ac.uk} - homepage: null - id: ehdaa - is_obsolete: true - layout: ontology_detail - replaced_by: ehdaa2 - taxon: {id: 'NCBITaxon:9606', label: Homo sapiens} - title: Human developmental anatomy, abstract version - build: {checkout: 'git clone https://github.com/obophenotype/human-developmental-anatomy-ontology.git', method: vcs, path: src/ontology, system: git} contact: {email: J.Bard@ed.ac.uk, label: Jonathan Bard} @@ -642,12 +752,6 @@ ontologies: - {id: ero.owl, ontology_purl: 'http://purl.obolibrary.org/obo/ero.owl'} title: eagle-i resource ontology tracker: http://code.google.com/p/eagle-i/issues/list -- contact: {email: eVOC mailing list, label: evoc@sanbi.ac.za} - homepage: http://www.evocontology.org/ - id: ev - is_obsolete: true - layout: ontology_detail - title: eVOC (Expressed Sequence Annotation for Humans) - build: {method: obo2owl, source_url: 'http://ctdbase.org/reports/CTD_exposure_ontology.obo'} description: Vocabularies for describing exposure data to inform understanding of environmental health. @@ -756,19 +860,6 @@ ontologies: taxon: {id: 'NCBITaxon:7227', label: Drosophila} title: Drosophila development tracker: http://purl.obolibrary.org/obo/fbdv/tracker -- build: {method: obo2owl, source_url: 'http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/taxonomy/fly_taxonomy.obo'} - contact: {email: mmc46@gen.cam.ac.uk, label: Marta Costa} - description: The taxonomy of the family Drosophilidae (largely after Baechli) - and of other taxa referred to in FlyBase. - domain: taxonomy - homepage: http://www.flybase.org/ - id: fbsp - is_obsolete: true - layout: ontology_detail - products: - - {id: fbsp.owl, ontology_purl: 'http://purl.obolibrary.org/obo/fbsp.owl'} - taxon: {id: 'NCBITaxon:7227', label: Drosophila} - title: Fly taxonomy - contact: {email: hastings@ebi.ac.uk, label: Janna Hastings} description: An ontology of physico-chemical methods and properties. id: fix @@ -846,63 +937,6 @@ ontologies: - {id: geo.owl, ontology_purl: 'http://purl.obolibrary.org/obo/geo.owl'} title: Geographical Entity Ontology tracker: https://ontology.atlassian.net/browse/GEO#selectedTab=com.atlassian.jira.plugin.system.project%3Aissues-panel -- browsers: - - {label: AmiGO, title: Gene Ontology AmiGO 2 Browser, url: 'http://amigo.geneontology.org/amigo/term/GO:0008150#display-lineage-tab'} - build: {checkout: 'svn --ignore-externals co svn://ext.geneontology.org/trunk/ontology', - infallible: 1, method: vcs, system: svn} - dependencies: - - {id: uberon, subset: go/extensions/uberon_import.owl} - - {id: cl, subset: go/extensions/cl_import.owl} - - {id: ncbitaxon, subset: go/extensions/ncbitaxon_import.owl} - - {id: ro, subset: go/extensions/ro_import.owl} - - connects: - - {id: nifstd} - - {id: go} - description: Bridging axioms between nifstd and go - id: go/extensions/go-bridge-to-nifstd.owl - publications: - - {id: 'http://www.ncbi.nlm.nih.gov/pubmed/24093723', title: 'The Gene Ontology - (GO) Cellular Component Ontology: integration with SAO (Subcellular Anatomy - Ontology) and other recent developments.'} - title: GO bridge to NIFSTD - type: BridgeOntology - depicted_by: http://geneontology.org/sites/default/files/go-logo-icon.mini__0.png - description: An ontology for describing the function of genes and gene products - domain: biology - facebook: https://www.facebook.com/Gene-Ontology-305908656519/ - id: go - in_foundry_order: 1 - integration_server: http://build.berkeleybop.org/view/GO - label: GO - layout: ontology_detail - license: {label: CC-BY, logo: 'http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png', - url: 'http://creativecommons.org/licenses/by/3.0/'} - ontology_purl: http://purl.obolibrary.org/obo/go.owl - products: - - {id: go.owl, ontology_purl: 'http://purl.obolibrary.org/obo/go.owl'} - - {description: The core ontology plus axioms connecting to select external ontologies, - id: go/extensions/go-plus.owl, ontology_purl: 'http://purl.obolibrary.org/obo/go/extensions/go-plus.owl', - title: GO-Plus} - - {description: Classes added to ncbitaxon for groupings such as prokaryotes, id: go/extensions/go-taxon-groupings.owl, - ontology_purl: 'http://purl.obolibrary.org/obo/go/extensions/go-taxon-groupings.owl', - title: GO Taxon Groupings} - taxon: {id: 'NCBITaxon:1', label: All life} - termgenie: http://go.termgenie.org - title: Gene Ontology - tracker: https://github.com/geneontology/go-ontology/issues/ - twitter: news4go -- contact: {email: Plant Ontology Administrators, label: po-discuss@plantontology.org} - homepage: http://www.gramene.org/plant_ontology/ - id: gro - is_obsolete: true - layout: ontology_detail - title: Cereal Plant Gross Anatomy -- contact: {email: Peter Midford, label: peteremidford@yahoo.com} - homepage: http://www.mesquiteproject.org/ontology/Habronattus/index.html - id: habronattus - is_obsolete: true - layout: ontology_detail - title: Habronattus courtship - build: {checkout: 'svn co http://obo.svn.sourceforge.net/svnroot/obo/ontologies/trunk/HAO', method: vcs, system: svn} contact: {email: diapriid@gmail.com, label: Matt Yoder} @@ -1028,20 +1062,6 @@ ontologies: products: - {id: idomal.owl, ontology_purl: 'http://purl.obolibrary.org/obo/idomal.owl'} title: Malaria Ontology -- {homepage: 'http://www.inoh.org', id: iev, is_obsolete: true, layout: ontology_detail, - title: Event (INOH pathway ontology)} -- contact: {email: INOH curators, label: curator@inoh.org} - homepage: http://www.inoh.org - id: imr - is_obsolete: true - layout: ontology_detail - title: Molecule role (INOH Protein name/family name ontology) -- contact: {email: InterPro Help, label: interhelp@ebi.ac.uk} - homepage: http://www.ebi.ac.uk/interpro/index.html - id: ipr - is_obsolete: true - layout: ontology_detail - title: Protein Domains - build: {method: owl2obo, source_url: 'http://svn.code.sf.net/p/kisao/code/tags/kisao-owl-latest/kisao.owl'} contact: {email: biomodels-net-support@lists.sf.net, label: The Biomodels.net team} description: A classification of algorithms available for the simulation of models @@ -1055,21 +1075,6 @@ ontologies: products: - {id: kisao.owl, ontology_purl: 'http://purl.obolibrary.org/obo/kisao.owl'} title: Kinetic Simulation Algorithm Ontology -- build: {method: owl2obo, source_url: 'http://www.lipidprofiles.com/LipidOntology'} - contact: {email: bakerc@unb.ca, label: Christipher Baker} - description: An ontology representation of the LIPIDMAPS nomenclature classification. - domain: lipids - id: lipro - in_foundry: false - is_obsolete: true - layout: ontology_detail - title: Lipid Ontology -- contact: {email: Peter Midford, label: peteremidford@yahoo.com} - homepage: http://www.mesquiteproject.org/ontology/Loggerhead/index.html - id: loggerhead - is_obsolete: true - layout: ontology_detail - title: Loggerhead nesting - build: {infallible: 1, method: obo2owl, source_url: 'ftp://ftp.informatics.jax.org/pub/reports/adult_mouse_anatomy.obo'} contact: {email: Terry.Hayamizu@jax.org, label: Terry Hayamizu} description: A structured controlled vocabulary of the adult anatomy of the mouse @@ -1101,18 +1106,6 @@ ontologies: - {id: mamo.owl, ontology_purl: 'http://purl.obolibrary.org/obo/mamo.owl'} title: Mathematical modeling ontology tracker: http://sourceforge.net/p/mamo-ontology/tickets/ -- contact: {email: Julie Thompson, label: julie@igbmc.u-strasbg.fr} - homepage: http://www-igbmc.u-strasbg.fr/BioInfo/MAO/mao.html - id: mao - is_obsolete: true - layout: ontology_detail - title: Multiple alignment -- contact: {email: Jonathan Bard, label: j.bard@ed.ac.uk} - homepage: null - id: mat - is_obsolete: true - layout: ontology_detail - title: Minimal anatomical terminology - build: {method: owl2obo, source_url: 'http://purl.obolibrary.org/obo/mf.owl'} contact: {email: hastings@ebi.ac.uk, label: Janna Hastings} homepage: https://code.google.com/p/mental-functioning-ontology/ @@ -1268,19 +1261,6 @@ ontologies: - {id: mmusdv.owl, ontology_purl: 'http://purl.obolibrary.org/obo/mmusdv.owl'} - {id: mmusdv.obo, ontology_purl: 'http://purl.obolibrary.org/obo/mmusdv.obo'} title: Mouse Developmental Stages -- contact: {email: stoeckrt@pcbi.upenn.edu, label: Chris Stoeckert} - description: A standardized description of a microarray experiment in support of - MAGE v.1. - domain: experiments - homepage: http://mged.sourceforge.net/ontologies/MGEDontology.php - id: mo - is_obsolete: true - layout: ontology_detail - page: http://mged.sourceforge.net/software/downloads.php - products: - - {id: mo.owl, ontology_purl: 'http://purl.obolibrary.org/obo/mo.owl'} - replaced_by: obi - title: Microarray experimental conditions - build: {method: obo2owl, source_url: 'https://raw.githubusercontent.com/MICommunity/psidev/master/psi/mod/data/PSI-MOD.obo'} contact: {email: hhe@ebi.ac.uk, label: Henning Hermjakob} description: PSI-MOD is an ontology consisting of terms that describe protein chemical @@ -1428,61 +1408,26 @@ ontologies: layout: ontology_detail title: NCI Thesaurus uri_prefix: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl# -- contact: {email: Fahim Imam, label: smtifahim@gmail.com} - description: Neuronal cell types - homepage: http://neuinfo.org/ - id: nif_cell - is_obsolete: true +- build: {method: owl2obo, source_url: 'http://svn.code.sf.net/p/oae/code/trunk/src/ontology/oae.owl'} + contact: {email: yongqunh@med.umich.edu, label: Yongqunh He} + description: A biomedical ontology in the domain of adverse events + domain: adverse events, health + homepage: http://www.oae-ontology.org + id: oae layout: ontology_detail - replaced_by: cl - title: NIF Cell -- contact: {email: Fahim Imam, label: smtifahim@gmail.com} - homepage: http://neuinfo.org/ - id: nif_dysfunction - is_obsolete: true - layout: ontology_detail - replaced_by: doid - title: NIF Dysfunction -- contact: {email: Fahim Imam, label: smtifahim@gmail.com} - homepage: http://neuinfo.org/ - id: nif_grossanatomy - is_obsolete: true - layout: ontology_detail - replaced_by: uberon - title: NIF Gross Anatomy -- build: {method: owl2obo, source_url: 'https://msi-workgroups.svn.sourceforge.net/svnroot/msi-workgroups/ontology/NMR.owl'} - contact: {email: schober@imbi.uni-freiburg.de, label: Schober Daniel} - description: Descriptors relevant to the experimental conditions of the Nuclear - Magnetic Resonance (NMR) component in a metabolomics investigation. - domain: experiments - homepage: http://msi-ontology.sourceforge.net/ - id: nmr - is_obsolete: true - layout: ontology_detail - page: http://msi-ontology.sourceforge.net/ontology/NMR.owlDocument.doc - products: - - {id: nmr.owl, ontology_purl: 'http://purl.obolibrary.org/obo/nmr.owl'} - title: NMR-instrument specific component of metabolomics investigations -- build: {method: owl2obo, source_url: 'http://svn.code.sf.net/p/oae/code/trunk/src/ontology/oae.owl'} - contact: {email: yongqunh@med.umich.edu, label: Yongqunh He} - description: A biomedical ontology in the domain of adverse events - domain: adverse events, health - homepage: http://www.oae-ontology.org - id: oae - layout: ontology_detail - license: {label: CC-BY, logo: 'http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png', - url: 'http://creativecommons.org/licenses/by/3.0/'} - ontology_purl: http://purl.obolibrary.org/obo/oae.owl - products: - - {id: oae.owl, ontology_purl: 'http://purl.obolibrary.org/obo/oae.owl'} - title: Ontology of Adverse Events -- build: {infallible: 0, method: archive, path: archive/src/ontology, source_url: 'http://build.berkeleybop.org/job/build-oba/lastSuccessfulBuild/artifact/*zip*/archive.zip'} - contact: {email: cjmungall@lbl.gov, label: Chris Mungall} - description: A collection of biological attributes (traits) covering all kingdoms - of life. - domain: phenotype - homepage: https://github.com/obophenotype/bio-attribute-ontology - id: oba + license: {label: CC-BY, logo: 'http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png', + url: 'http://creativecommons.org/licenses/by/3.0/'} + ontology_purl: http://purl.obolibrary.org/obo/oae.owl + products: + - {id: oae.owl, ontology_purl: 'http://purl.obolibrary.org/obo/oae.owl'} + title: Ontology of Adverse Events +- build: {infallible: 0, method: archive, path: archive/src/ontology, source_url: 'http://build.berkeleybop.org/job/build-oba/lastSuccessfulBuild/artifact/*zip*/archive.zip'} + contact: {email: cjmungall@lbl.gov, label: Chris Mungall} + description: A collection of biological attributes (traits) covering all kingdoms + of life. + domain: phenotype + homepage: https://github.com/obophenotype/bio-attribute-ontology + id: oba layout: ontology_detail ontology_purl: http://purl.obolibrary.org/obo/oba.owl page: http://wiki.geneontology.org/index.php/Extensions/x-attribute @@ -1504,29 +1449,6 @@ ontologies: - {id: obcs.owl, ontology_purl: 'http://purl.obolibrary.org/obo/obcs.owl'} title: Ontology of Biological and Clinical Statistics tracker: https://github.com/obcs/obcs/issues -- browsers: - - {label: BioPortal, title: BioPortal Browser, url: 'http://bioportal.bioontology.org/ontologies/OBI?p=classes'} - build: {source_url: 'http://purl.obofoundry.org/obo/obi/repository/trunk/src/ontology/branches/'} - contact: {email: bpeters@liai.org, label: Bjoern Peters} - depicted_by: https://svn.code.sf.net/p/obi/code/trunk/web/htdocs/images/obi-lotext.png - description: An integrated ontology for the description of life-science and clinical - investigations - domain: experiments - homepage: http://obi-ontology.org - id: obi - in_foundry_order: 1 - integration_server: http://build.berkeleybop.org/job/build-obi/ - layout: ontology_detail - license: {label: CC-BY, logo: 'http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png', - url: 'http://creativecommons.org/licenses/by/3.0/'} - mailing_list: http://groups.google.com/group/obi-users - ontology_purl: http://purl.obolibrary.org/obo/obi.owl - products: - - {id: obi.owl, ontology_purl: 'http://purl.obolibrary.org/obo/obi.owl', title: OBI} - - {id: obi/obi_core.owl, ontology_purl: 'http://purl.obolibrary.org/obo/obi/obi_core.owl', - title: OBI Core} - title: Ontology for Biomedical Investigations - tracker: http://purl.obofoundry.org/obo/obi/tracker - contact: {email: jiezheng@upenn.edu, label: Jie Zheng} description: An ontology built for annotation and modeling of biobank repository and biobanking administration @@ -1541,13 +1463,6 @@ ontologies: - {id: obib.owl, ontology_purl: 'http://purl.obolibrary.org/obo/obib.owl'} title: Ontology for Biobanking tracker: https://github.com/biobanking/biobanking/issues -- contact: {email: Chris Mungall, label: cjmungall@lbl.gov} - homepage: http://www.obofoundry.org/ro - id: obo_rel - is_obsolete: true - layout: ontology_detail - replaced_by: ro - title: OBO relationship types (legacy) - contact: {email: yongqunh@med.umich.edu, label: Yongqun Oliver He} description: A formal ontology of genes and genomes of biological organisms. homepage: http://ogg.googlecode.com/ @@ -1665,36 +1580,6 @@ ontologies: products: - {id: ovae.owl, ontology_purl: 'http://purl.obolibrary.org/obo/ovae.owl'} title: Ontology of Vaccine Adverse Events -- contact: {email: Pankaj Jaiswal, label: jaiswalp@science.oregonstate.edu} - homepage: http://www.plantontology.org - id: pao - is_obsolete: true - layout: ontology_detail - taxon: {id: 'NCBITaxon:33090', label: Viridiplantae} - title: Plant Anatomy Ontology -- browsers: - - {label: Aber-OWL, title: Aber-OWL Ontology Browser, url: 'http://aber-owl.net/ontology/PATO'} - - {label: BioPortal, title: BioPortal Ontology Browser, url: 'https://bioportal.bioontology.org/ontologies/PATO'} - - {label: OntoBee, title: OntoBee Browser, url: 'http://www.ontobee.org/browser/index.php?o=PATO'} - build: {infallible: 1, method: obo2owl, source_url: 'https://raw.githubusercontent.com/pato-ontology/pato/master/pato.obo'} - contact: {email: g.gkoutos@gmail.com, label: George Gkoutos} - description: An ontology of phenotypic qualities (properties, attributes or characteristics) - domain: phenotype - homepage: https://github.com/pato-ontology/pato/ - id: pato - in_foundry_order: 1 - jobs: - - {id: 'http://build.berkeleybop.org/job/build-pato', type: DryRunBuild} - layout: ontology_detail - license: {label: CC-BY, logo: 'http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png', - url: 'http://creativecommons.org/licenses/by/3.0/'} - ontology_purl: http://purl.obolibrary.org/obo/pato.owl - products: - - {id: pato.owl, ontology_purl: 'http://purl.obolibrary.org/obo/pato.owl'} - - {id: pato.obo, ontology_purl: 'http://purl.obolibrary.org/obo/pato.obo'} - repository: https://github.com/pato-ontology/pato/ - title: Phenotypic quality - tracker: https://github.com/pato-ontology/pato/issues - build: {method: owl2obo, oort_args: --no-subsets --reasoner hermit, source_url: 'http://purl.obolibrary.org/obo/pco.owl'} contact: {email: rwalls2008@gmail.com, label: Ramona Walls} description: A taxon-neutral ontology of material entities, qualities, and processes @@ -1707,14 +1592,6 @@ ontologies: - {id: pco.owl, ontology_purl: 'http://purl.obolibrary.org/obo/pco.owl'} title: Population and Community Ontology tracker: https://github.com/PopulationAndCommunityOntology/pco/issues -- contact: {email: Thorsten Heinrich, label: henrich@embl.de} - homepage: http://4dx.embl.de/platy - id: pd_st - is_obsolete: true - layout: ontology_detail - replaced_by: pdumdv - taxon: {id: 'NCBITaxon:6358', label: Platynereis} - title: Platynereis stage ontology - build: {method: obo2owl, source_url: 'https://raw.githubusercontent.com/obophenotype/developmental-stage-ontologies/master/src/pdumdv/pdumdv.obo'} description: Life cycle stages for Mus Musculus homepage: https://github.com/obophenotype/developmental-stage-ontologies/wiki/PdumDv @@ -1728,45 +1605,6 @@ ontologies: - {id: pdumdv.owl, ontology_purl: 'http://purl.obolibrary.org/obo/pdumdv.owl'} - {id: pdumdv.obo, ontology_purl: 'http://purl.obolibrary.org/obo/pdumdv.obo'} title: Platynereis Developmental Stages -- contact: {email: Plant Ontology Administrators, label: po-discuss@plantontology.org} - homepage: http://www.plantontology.org - id: pgdso - is_obsolete: true - layout: ontology_detail - taxon: {id: 'NCBITaxon:33090', label: Viridiplantae} - title: Plant Growth and Development Stage -- contact: {email: Matt Berriman, label: mb4@sanger.ac.uk} - homepage: http://www.sanger.ac.uk/Users/mb4/PLO/ - id: plo - is_obsolete: true - layout: ontology_detail - title: Plasmodium life cycle -- build: {infallible: 1, method: obo2owl, notes: switch to vcs method, source_url: 'https://raw.githubusercontent.com/Planteome/plant-ontology/master/po-release-files/plant_ontology.obo'} - contact: {email: jaiswalp@science.oregonstate.edu, label: Pankaj Jaiswal} - description: The Plant Ontology is a structured vocabulary and database resource - that links plant anatomy, morphology and growth and development to plant genomics - data. - domain: anatomy and development - homepage: http://www.plantontology.org - id: po - in_foundry_order: 1 - layout: ontology_detail - license: {label: CC-BY, logo: 'http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png', - url: 'http://creativecommons.org/licenses/by/3.0/'} - ontology_purl: http://purl.obolibrary.org/obo/po.owl - page: http://www.plantontology.org/amigo/go.cgi - products: - - {id: po.owl, ontology_purl: 'http://purl.obolibrary.org/obo/po.owl'} - - {id: po.obo, ontology_purl: 'http://purl.obolibrary.org/obo/po.obo'} - publications: - - {id: 'http://www.ncbi.nlm.nih.gov/pubmed/23220694', title: The plant ontology - as a tool for comparative plant anatomy and genomic analyses.} - - {id: 'http://www.ncbi.nlm.nih.gov/pubmed/22847540', title: Ontologies as integrative - tools for plant science.} - taxon: {id: 'NCBITaxon:33090', label: Viridiplantae} - title: Plant Ontology - tracker: https://github.com/Planteome/plant-ontology/issues - twitter: planteome - build: {checkout: 'git clone https://github.com/obophenotype/porifera-ontology.git', infallible: 1, method: vcs, path: ., system: git} contact: {email: robert.thacker@stonybrook.edu, label: Bob Thacker} @@ -1787,27 +1625,6 @@ ontologies: taxon: {id: 'NCBITaxon:6040', label: Porifera} title: Porifera Ontology tracker: https://github.com/obophenotype/porifera-ontology/issues -- build: {infallible: 0, method: obo2owl, oort_args: --no-reasoner, source_url: 'ftp://ftp.pir.georgetown.edu/databases/ontology/pro_obo/pro.obo'} - contact: {email: dan5@georgetown.edu, label: Darren Natale} - description: an ontological representation of protein-related entities - development: {id_policy: 'https://pir17.georgetown.edu/confluence/display/PROWIKI/PRO+URI+policy'} - documentation: ftp://ftp.pir.georgetown.edu/databases/ontology/pro_obo/pro_readme.txt - domain: proteins - homepage: http://proconsortium.org - id: pr - in_foundry_order: 1 - layout: ontology_detail - ontology_purl: http://purl.obolibrary.org/obo/pr.owl - products: - - {id: pr.owl, ontology_purl: 'http://purl.obolibrary.org/obo/pr.owl'} - title: PRotein Ontology (PRO) - tracker: http://sourceforge.net/tracker/?group_id=266825&atid=1135711 -- contact: {email: Satya S. Sahoo, label: satya30@uga.edu} - homepage: http://lsdis.cs.uga.edu/projects/glycomics/propreo/ - id: propreo - is_obsolete: true - layout: ontology_detail - title: Proteomics data and process provenance - browsers: - {label: RGD, title: RGD Ontology Browser, url: 'http://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=PW:0000001'} build: {method: obo2owl, source_url: 'ftp://ftp.rgd.mcw.edu/pub/data_release/ontology_obo_files/pathway/pathway.obo'} @@ -1828,14 +1645,6 @@ ontologies: - {id: 'http://www.ncbi.nlm.nih.gov/pubmed/24499703', title: The pathway ontology - updates and applications.} title: Pathway ontology -- contact: {email: john.garavelli@ebi.ac.uk, label: John Garavelli} - description: For the description of covalent bonds in proteins. - domain: proteins - homepage: http://www.ebi.ac.uk/RESID/ - id: resid - is_obsolete: true - layout: ontology_detail - title: Protein covalent bond - build: {method: obo2owl, source_url: 'http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/physicochemical/rex.obo'} contact: {email: hastings@ebi.ac.uk, label: Janna Hastings} description: An ontology of physico-chemical processes, i.e. physico-chemical changes @@ -1919,14 +1728,6 @@ ontologies: - {id: rxno.owl, ontology_purl: 'http://purl.obolibrary.org/obo/rxno.owl', title: Name Reaction Ontology} title: Name Reaction Ontology -- contact: {email: Stephen Larson, label: slarson@ncmir.ucsd.edu} - homepage: http://ccdb.ucsd.edu/CCDBWebSite/sao.html - id: sao - is_obsolete: true - layout: ontology_detail - replaced_by: go - taxon: {id: 'NCBITaxon:9606', label: Homo sapiens} - title: Subcellular anatomy ontology - build: {method: obo2owl, source_url: 'http://www.ebi.ac.uk/sbo/exports/Main/SBO_OBO.obo'} contact: {email: biomodels-net-support@lists.sf.net, label: The Biomodels.net team} description: Terms commonly used in Systems Biology, and in particular in computational @@ -1991,13 +1792,6 @@ ontologies: Ontology terms and relationships.} title: Sequence types and features tracker: https://github.com/The-Sequence-Ontology/SO-Ontologies/issues -- contact: {email: Adrien Coulet, label: Adrien.Coulet@loria.fr} - homepage: http://www.loria.fr/~coulet/sopharm2.0_description.php - id: sopharm - is_obsolete: true - layout: ontology_detail - taxon: {id: 'NCBITaxon:9606', label: Homo sapiens} - title: Suggested Ontology for Pharmacogenomics - build: {method: obo2owl, source_url: 'http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/spider/spider_comparative_biology.obo'} contact: {email: ramirez@macn.gov.ar, label: Martin Ramirez} description: An ontology for spider comparative biology including anatomical parts @@ -2073,35 +1867,6 @@ ontologies: - {id: tads.owl, ontology_purl: 'http://purl.obolibrary.org/obo/tads.owl'} taxon: {id: 'NCBITaxon:6939', label: Ixodidae} title: Tick gross anatomy -- contact: {email: Pierre Sprumont, label: pierre.sprumont@unifr.ch} - homepage: null - id: tahe - is_obsolete: true - layout: ontology_detail - taxon: {id: 'NCBITaxon:9606', label: Homo sapiens} - title: Terminology of Anatomy of Human Embryology -- contact: {email: Pierre Sprumont, label: pierre.sprumont@unifr.ch} - homepage: null - id: tahh - is_obsolete: true - layout: ontology_detail - taxon: {id: 'NCBITaxon:9606', label: Homo sapiens} - title: Terminology of Anatomy of Human Histology -- build: {method: obo2owl, source_url: 'http://purl.obolibrary.org/obo/tao.obo'} - contact: {email: wasila.dahdul@usd.edu, label: Wasila Dahdul} - description: Multispecies fish anatomy ontology. Originally seeded from ZFA, but - intended to cover terms relevant to other taxa - domain: anatomy - homepage: http://wiki.phenoscape.org/wiki/Teleost_Anatomy_Ontology - id: tao - is_obsolete: true - layout: ontology_detail - products: - - {id: tao.owl, ontology_purl: 'http://purl.obolibrary.org/obo/tao.owl'} - replaced_by: uberon - taxon: {id: 'NCBITaxon:32443', label: Teleostei} - title: Teleost Anatomy Ontology - tracker: https://github.com/obophenotype/uberon/issues?q=is%3Aissue+label%3ATAO - build: {method: obo2owl, source_url: 'https://raw.github.com/obophenotype/taxonomic-rank-ontology/master/src/ontology/taxrank.obo'} contact: {email: peteremidford@yahoo.com, label: Peter Midford} description: A vocabulary of taxonomic ranks (species, family, phylum, etc) @@ -2291,13 +2056,6 @@ ontologies: products: - {id: vario.owl, ontology_purl: 'http://purl.obolibrary.org/obo/vario.owl'} title: Variation Ontology -- id: vhog - is_obsolete: true - layout: ontology_detail - products: - - {id: vhog.owl, ontology_purl: 'http://purl.obolibrary.org/obo/vhog.owl'} - replaced_by: uberon - title: Vertebrate Homologous Ontology Group Ontology - build: {method: obo2owl, source_url: 'http://www.violinet.org/vo'} contact: {email: yongqunh@med.umich.edu, label: Yongqunh He} description: a biomedical ontology in the domain of vaccine and vaccination @@ -2313,21 +2071,6 @@ ontologies: - {id: vo.owl, ontology_purl: 'http://purl.obolibrary.org/obo/vo.owl'} title: Vaccine Ontology tracker: http://sourceforge.net/tracker/?atid=1127137&group_id=255029&func=browse -- build: {method: obo2owl, source_url: 'http://phenoscape.svn.sourceforge.net/svnroot/phenoscape/tags/vocab-releases/VSAO/vsao.obo'} - contact: {email: wasila.dahdul@usd.edu, label: Wasila Dahdul} - description: Vertebrate skeletal anatomy ontology. - domain: anatomy - homepage: https://www.nescent.org/phenoscape/Main_Page - id: vsao - is_obsolete: true - layout: ontology_detail - page: https://www.phenoscape.org/wiki/Skeletal_Anatomy_Jamboree - products: - - {id: vsao.owl, ontology_purl: 'http://purl.obolibrary.org/obo/vsao.owl'} - replaced_by: uberon - taxon: {id: 'NCBITaxon:7742', label: Vertebrata} - title: Vertebrate Skeletal Anatomy Ontology- - tracker: https://github.com/obophenotype/uberon/issues?q=is%3Aissue+label%3AVSAO - build: {checkout: 'svn co http://phenotype-ontologies.googlecode.com/svn/trunk/src/ontology/vt', method: vcs, system: svn} description: An ontology of traits covering vertebrates @@ -2384,36 +2127,15 @@ ontologies: - {id: wbphenotype.owl, ontology_purl: 'http://purl.obolibrary.org/obo/wbphenotype.owl'} taxon: {id: 'NCBITaxon:6237', label: Caenorhabditis} title: C. elegans phenotype -- build: {infallible: 0, method: obo2owl, source_url: 'https://raw.githubusercontent.com/xenopus-anatomy/xao/master/xenopus_anatomy.obo'} - description: Anatomy and development of the African clawed frog (Xenopus laevis). - domain: anatomy - homepage: http://www.xenbase.org/anatomy/xao.do?method=display - id: xao - in_foundry_order: 1 - layout: ontology_detail - license: {label: CC-BY, logo: 'http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png', - url: 'http://creativecommons.org/licenses/by/3.0/'} - ontology_purl: http://purl.obolibrary.org/obo/xao.owl - products: - - {id: xao.owl, ontology_purl: 'http://purl.obolibrary.org/obo/xao.owl'} - publications: - - {id: 'http://www.ncbi.nlm.nih.gov/pubmed/18817563', title: An ontology for Xenopus - anatomy and development.} - - {id: 'http://www.ncbi.nlm.nih.gov/pubmed/24139024', title: 'Enhanced XAO: the - ontology of Xenopus anatomy and development underpins more accurate annotation - of gene expression and queries on Xenbase.'} - taxon: {id: 'NCBITaxon:8353', label: Xenopus} - title: Xenopus anatomy and development - tracker: https://github.com/xenopus-anatomy/xao/issues -- browsers: - - {label: RGD, title: RGD Ontology Browser, url: 'http://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=XCO:0000000'} - build: {method: obo2owl, source_url: 'ftp://ftp.rgd.mcw.edu/pub/ontology/experimental_condition/experimental_condition.obo'} - contact: {email: shimoyama@mcw.edu, label: Mary Shimoyama} - description: Conditions under which physiological and morphological measurements - are made both in the clinic and in studies involving humans or model organisms. - domain: clinical - homepage: ['http://rgd.mcw.edu/rgdweb/ontology/search.html', 'ftp://ftp.rgd.mcw.edu/pub/ontology/experimental_condition/'] - id: xco +- browsers: + - {label: RGD, title: RGD Ontology Browser, url: 'http://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=XCO:0000000'} + build: {method: obo2owl, source_url: 'ftp://ftp.rgd.mcw.edu/pub/ontology/experimental_condition/experimental_condition.obo'} + contact: {email: shimoyama@mcw.edu, label: Mary Shimoyama} + description: Conditions under which physiological and morphological measurements + are made both in the clinic and in studies involving humans or model organisms. + domain: clinical + homepage: ['http://rgd.mcw.edu/rgdweb/ontology/search.html', 'ftp://ftp.rgd.mcw.edu/pub/ontology/experimental_condition/'] + id: xco layout: ontology_detail ontology_purl: http://purl.obolibrary.org/obo/xco.owl products: @@ -2426,42 +2148,6 @@ ontologies: measurement method and experimental condition ontologies: expansion, improvements and new applications.'} title: Experimental condition ontology -- contact: {email: Mike Cherry, label: cherry@genome.stanford.edu} - homepage: http://www.yeastgenome.org/ - id: ypo - is_obsolete: true - layout: ontology_detail - replaced_by: apo - taxon: {id: 'NCBITaxon:4932', label: Saccharomyces cerevisiae} - title: Yeast phenotypes -- contact: {email: Leszek Vincent, label: Leszek@missouri.edu} - homepage: http://www.maizemap.org/ - id: zea - is_obsolete: true - layout: ontology_detail - taxon: {id: 'NCBITaxon:4575', label: Zea} - title: Maize gross anatomy -- build: {infallible: 1, method: obo2owl, notes: may be ready to switch to vcs soon, - source_url: 'https://raw.githubusercontent.com/cerivs/zebrafish-anatomical-ontology/master/src/zebrafish_anatomy.obo'} - contact: {email: zfinadmin@zfin.org, label: ZFIN administrators} - description: A structured controlled vocabulary of the anatomy and development of - the Zebrafish - domain: anatomy - homepage: http://zfin.org/zf_info/anatomy/dict/sum.html - id: zfa - in_foundry_order: 1 - layout: ontology_detail - license: {label: CC-BY, logo: 'http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png', - url: 'http://creativecommons.org/licenses/by/3.0/'} - ontology_purl: http://purl.obolibrary.org/obo/zfa.owl - products: - - {id: zfa.owl, ontology_purl: 'http://purl.obolibrary.org/obo/zfa.owl'} - publications: - - {id: 'http://www.ncbi.nlm.nih.gov/pubmed/24568621', title: 'The zebrafish anatomy - and stage ontologies: representing the anatomy and development of Danio rerio.'} - taxon: {id: 'NCBITaxon:7954', label: Danio} - title: Zebrafish anatomy and development - tracker: https://github.com/cerivs/zebrafish-anatomical-ontology/issues - build: {infallible: 1, method: obo2owl, source_url: 'https://raw.githubusercontent.com/obophenotype/developmental-stage-ontologies/master/src/zfs/zfs.obo'} contact: {email: zfinadmin@zfin.org, label: ZFIN administrators} description: Developmental stages of the Zebrafish @@ -2478,6 +2164,320 @@ ontologies: - {id: zfs.owl, ontology_purl: 'http://purl.obolibrary.org/obo/zfs.owl'} taxon: {id: 'NCBITaxon:7954', label: Danio} title: Zebrafish developmental stages +- contact: {email: David Blackburn, label: david.c.blackburn@gmail.com} + homepage: http://github.com/seger/aao + id: aao + is_obsolete: true + layout: ontology_detail + replaced_by: uberon + taxon: {id: 'NCBITaxon:8292', label: Amphibia} + title: Amphibian gross anatomy +- contact: {email: Animal Diversity Web technical staff, label: adw_geeks@umich.edu} + homepage: http://www.animaldiversity.org + id: adw + is_obsolete: true + layout: ontology_detail + title: Animal natural history and life history +- contact: {email: David Blackburn, label: david.c.blackburn@gmail.com} + homepage: http://www.amphibanat.org + id: ato + is_obsolete: true + layout: ontology_detail + taxon: {id: 'NCBITaxon:8292', label: Amphibia} + title: Amphibian taxonomy +- build: {method: obo2owl, source_url: 'http://4dx.embl.de/4DXpress_4d/edocs/bilateria_mrca.obo'} + contact: {email: henrich@embl.de, label: Thorsten Heinrich} + domain: anatomy + homepage: http://4dx.embl.de/4DXpress + id: bila + is_obsolete: true + layout: ontology_detail + products: + - {id: bila.owl, ontology_purl: 'http://purl.obolibrary.org/obo/bila.owl'} + replaced_by: uberon + taxon: {id: 'NCBITaxon:33213', label: Bilateria} + title: Bilateria anatomy +- contact: {email: Vivian Lee, label: vlee@ebi.ac.uk} + homepage: http://www.ebi.ac.uk/Rebholz-srv/GRO/GRO.html + id: bootstrep + is_obsolete: true + layout: ontology_detail + replaced_by: molecular_function + title: Gene Regulation Ontology +- contact: {email: Lindsay Cowell, label: Lindsay.Cowell@utsouthwestern.edu} + homepage: http://www.dukeontologygroup.org/Projects.html + id: dc_cl + is_obsolete: true + layout: ontology_detail + replaced_by: cl + taxon: {id: all, label: null} + title: Dendritic cell +- contact: {email: Jonathan Bard, label: J.Bard@ed.ac.uk} + homepage: http://genex.hgu.mrc.ac.uk/ + id: ehda + is_obsolete: true + layout: ontology_detail + replaced_by: ehdaa2 + taxon: {id: 'NCBITaxon:9606', label: Homo sapiens} + title: Human developmental anatomy, timed version +- contact: {email: Jonathan Bard, label: J.Bard@ed.ac.uk} + homepage: null + id: ehdaa + is_obsolete: true + layout: ontology_detail + replaced_by: ehdaa2 + taxon: {id: 'NCBITaxon:9606', label: Homo sapiens} + title: Human developmental anatomy, abstract version +- contact: {email: eVOC mailing list, label: evoc@sanbi.ac.za} + homepage: http://www.evocontology.org/ + id: ev + is_obsolete: true + layout: ontology_detail + title: eVOC (Expressed Sequence Annotation for Humans) +- build: {method: obo2owl, source_url: 'http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/taxonomy/fly_taxonomy.obo'} + contact: {email: mmc46@gen.cam.ac.uk, label: Marta Costa} + description: The taxonomy of the family Drosophilidae (largely after Baechli) + and of other taxa referred to in FlyBase. + domain: taxonomy + homepage: http://www.flybase.org/ + id: fbsp + is_obsolete: true + layout: ontology_detail + products: + - {id: fbsp.owl, ontology_purl: 'http://purl.obolibrary.org/obo/fbsp.owl'} + taxon: {id: 'NCBITaxon:7227', label: Drosophila} + title: Fly taxonomy +- contact: {email: Plant Ontology Administrators, label: po-discuss@plantontology.org} + homepage: http://www.gramene.org/plant_ontology/ + id: gro + is_obsolete: true + layout: ontology_detail + title: Cereal Plant Gross Anatomy +- contact: {email: Peter Midford, label: peteremidford@yahoo.com} + homepage: http://www.mesquiteproject.org/ontology/Habronattus/index.html + id: habronattus + is_obsolete: true + layout: ontology_detail + title: Habronattus courtship +- {homepage: 'http://www.inoh.org', id: iev, is_obsolete: true, layout: ontology_detail, + title: Event (INOH pathway ontology)} +- contact: {email: INOH curators, label: curator@inoh.org} + homepage: http://www.inoh.org + id: imr + is_obsolete: true + layout: ontology_detail + title: Molecule role (INOH Protein name/family name ontology) +- contact: {email: InterPro Help, label: interhelp@ebi.ac.uk} + homepage: http://www.ebi.ac.uk/interpro/index.html + id: ipr + is_obsolete: true + layout: ontology_detail + title: Protein Domains +- build: {method: owl2obo, source_url: 'http://www.lipidprofiles.com/LipidOntology'} + contact: {email: bakerc@unb.ca, label: Christipher Baker} + description: An ontology representation of the LIPIDMAPS nomenclature classification. + domain: lipids + id: lipro + in_foundry: false + is_obsolete: true + layout: ontology_detail + title: Lipid Ontology +- contact: {email: Peter Midford, label: peteremidford@yahoo.com} + homepage: http://www.mesquiteproject.org/ontology/Loggerhead/index.html + id: loggerhead + is_obsolete: true + layout: ontology_detail + title: Loggerhead nesting +- contact: {email: Julie Thompson, label: julie@igbmc.u-strasbg.fr} + homepage: http://www-igbmc.u-strasbg.fr/BioInfo/MAO/mao.html + id: mao + is_obsolete: true + layout: ontology_detail + title: Multiple alignment +- contact: {email: Jonathan Bard, label: j.bard@ed.ac.uk} + homepage: null + id: mat + is_obsolete: true + layout: ontology_detail + title: Minimal anatomical terminology +- contact: {email: stoeckrt@pcbi.upenn.edu, label: Chris Stoeckert} + description: A standardized description of a microarray experiment in support of + MAGE v.1. + domain: experiments + homepage: http://mged.sourceforge.net/ontologies/MGEDontology.php + id: mo + is_obsolete: true + layout: ontology_detail + page: http://mged.sourceforge.net/software/downloads.php + products: + - {id: mo.owl, ontology_purl: 'http://purl.obolibrary.org/obo/mo.owl'} + replaced_by: obi + title: Microarray experimental conditions +- contact: {email: Fahim Imam, label: smtifahim@gmail.com} + description: Neuronal cell types + homepage: http://neuinfo.org/ + id: nif_cell + is_obsolete: true + layout: ontology_detail + replaced_by: cl + title: NIF Cell +- contact: {email: Fahim Imam, label: smtifahim@gmail.com} + homepage: http://neuinfo.org/ + id: nif_dysfunction + is_obsolete: true + layout: ontology_detail + replaced_by: doid + title: NIF Dysfunction +- contact: {email: Fahim Imam, label: smtifahim@gmail.com} + homepage: http://neuinfo.org/ + id: nif_grossanatomy + is_obsolete: true + layout: ontology_detail + replaced_by: uberon + title: NIF Gross Anatomy +- build: {method: owl2obo, source_url: 'https://msi-workgroups.svn.sourceforge.net/svnroot/msi-workgroups/ontology/NMR.owl'} + contact: {email: schober@imbi.uni-freiburg.de, label: Schober Daniel} + description: Descriptors relevant to the experimental conditions of the Nuclear + Magnetic Resonance (NMR) component in a metabolomics investigation. + domain: experiments + homepage: http://msi-ontology.sourceforge.net/ + id: nmr + is_obsolete: true + layout: ontology_detail + page: http://msi-ontology.sourceforge.net/ontology/NMR.owlDocument.doc + products: + - {id: nmr.owl, ontology_purl: 'http://purl.obolibrary.org/obo/nmr.owl'} + title: NMR-instrument specific component of metabolomics investigations +- contact: {email: Chris Mungall, label: cjmungall@lbl.gov} + homepage: http://www.obofoundry.org/ro + id: obo_rel + is_obsolete: true + layout: ontology_detail + replaced_by: ro + title: OBO relationship types (legacy) +- contact: {email: Pankaj Jaiswal, label: jaiswalp@science.oregonstate.edu} + homepage: http://www.plantontology.org + id: pao + is_obsolete: true + layout: ontology_detail + taxon: {id: 'NCBITaxon:33090', label: Viridiplantae} + title: Plant Anatomy Ontology +- contact: {email: Thorsten Heinrich, label: henrich@embl.de} + homepage: http://4dx.embl.de/platy + id: pd_st + is_obsolete: true + layout: ontology_detail + replaced_by: pdumdv + taxon: {id: 'NCBITaxon:6358', label: Platynereis} + title: Platynereis stage ontology +- contact: {email: Plant Ontology Administrators, label: po-discuss@plantontology.org} + homepage: http://www.plantontology.org + id: pgdso + is_obsolete: true + layout: ontology_detail + taxon: {id: 'NCBITaxon:33090', label: Viridiplantae} + title: Plant Growth and Development Stage +- contact: {email: Matt Berriman, label: mb4@sanger.ac.uk} + homepage: http://www.sanger.ac.uk/Users/mb4/PLO/ + id: plo + is_obsolete: true + layout: ontology_detail + title: Plasmodium life cycle +- contact: {email: Satya S. Sahoo, label: satya30@uga.edu} + homepage: http://lsdis.cs.uga.edu/projects/glycomics/propreo/ + id: propreo + is_obsolete: true + layout: ontology_detail + title: Proteomics data and process provenance +- contact: {email: john.garavelli@ebi.ac.uk, label: John Garavelli} + description: For the description of covalent bonds in proteins. + domain: proteins + homepage: http://www.ebi.ac.uk/RESID/ + id: resid + is_obsolete: true + layout: ontology_detail + title: Protein covalent bond +- contact: {email: Stephen Larson, label: slarson@ncmir.ucsd.edu} + homepage: http://ccdb.ucsd.edu/CCDBWebSite/sao.html + id: sao + is_obsolete: true + layout: ontology_detail + replaced_by: go + taxon: {id: 'NCBITaxon:9606', label: Homo sapiens} + title: Subcellular anatomy ontology +- contact: {email: Adrien Coulet, label: Adrien.Coulet@loria.fr} + homepage: http://www.loria.fr/~coulet/sopharm2.0_description.php + id: sopharm + is_obsolete: true + layout: ontology_detail + taxon: {id: 'NCBITaxon:9606', label: Homo sapiens} + title: Suggested Ontology for Pharmacogenomics +- contact: {email: Pierre Sprumont, label: pierre.sprumont@unifr.ch} + homepage: null + id: tahe + is_obsolete: true + layout: ontology_detail + taxon: {id: 'NCBITaxon:9606', label: Homo sapiens} + title: Terminology of Anatomy of Human Embryology +- contact: {email: Pierre Sprumont, label: pierre.sprumont@unifr.ch} + homepage: null + id: tahh + is_obsolete: true + layout: ontology_detail + taxon: {id: 'NCBITaxon:9606', label: Homo sapiens} + title: Terminology of Anatomy of Human Histology +- build: {method: obo2owl, source_url: 'http://purl.obolibrary.org/obo/tao.obo'} + contact: {email: wasila.dahdul@usd.edu, label: Wasila Dahdul} + description: Multispecies fish anatomy ontology. Originally seeded from ZFA, but + intended to cover terms relevant to other taxa + domain: anatomy + homepage: http://wiki.phenoscape.org/wiki/Teleost_Anatomy_Ontology + id: tao + is_obsolete: true + layout: ontology_detail + products: + - {id: tao.owl, ontology_purl: 'http://purl.obolibrary.org/obo/tao.owl'} + replaced_by: uberon + taxon: {id: 'NCBITaxon:32443', label: Teleostei} + title: Teleost Anatomy Ontology + tracker: https://github.com/obophenotype/uberon/issues?q=is%3Aissue+label%3ATAO +- id: vhog + is_obsolete: true + layout: ontology_detail + products: + - {id: vhog.owl, ontology_purl: 'http://purl.obolibrary.org/obo/vhog.owl'} + replaced_by: uberon + title: Vertebrate Homologous Ontology Group Ontology +- build: {method: obo2owl, source_url: 'http://phenoscape.svn.sourceforge.net/svnroot/phenoscape/tags/vocab-releases/VSAO/vsao.obo'} + contact: {email: wasila.dahdul@usd.edu, label: Wasila Dahdul} + description: Vertebrate skeletal anatomy ontology. + domain: anatomy + homepage: https://www.nescent.org/phenoscape/Main_Page + id: vsao + is_obsolete: true + layout: ontology_detail + page: https://www.phenoscape.org/wiki/Skeletal_Anatomy_Jamboree + products: + - {id: vsao.owl, ontology_purl: 'http://purl.obolibrary.org/obo/vsao.owl'} + replaced_by: uberon + taxon: {id: 'NCBITaxon:7742', label: Vertebrata} + title: Vertebrate Skeletal Anatomy Ontology- + tracker: https://github.com/obophenotype/uberon/issues?q=is%3Aissue+label%3AVSAO +- contact: {email: Mike Cherry, label: cherry@genome.stanford.edu} + homepage: http://www.yeastgenome.org/ + id: ypo + is_obsolete: true + layout: ontology_detail + replaced_by: apo + taxon: {id: 'NCBITaxon:4932', label: Saccharomyces cerevisiae} + title: Yeast phenotypes +- contact: {email: Leszek Vincent, label: Leszek@missouri.edu} + homepage: http://www.maizemap.org/ + id: zea + is_obsolete: true + layout: ontology_detail + taxon: {id: 'NCBITaxon:4575', label: Zea} + title: Maize gross anatomy principles: - {id: fp-000-summary, layout: principle, title: summary} - {id: fp-001-open, layout: principle, title: open} diff --git a/_includes/ontology_table.html b/_includes/ontology_table.html index 49e0ce9e0..0d29dd023 100644 --- a/_includes/ontology_table.html +++ b/_includes/ontology_table.html @@ -1,9 +1,8 @@ Download table as: [ YAML | JSON-LD | RDF/Turtle ] - {% assign sorted_ontologies = site.ontologies | sort: 'in_foundry_order', 'last' %} - {% for ont in sorted_ontologies %} - + {% for ont in site.ontologies %} +
{% if ont.is_obsolete %} diff --git a/_includes/themes/bootstrap-3/default.html b/_includes/themes/bootstrap-3/default.html index 0e27dd515..3a076c521 100644 --- a/_includes/themes/bootstrap-3/default.html +++ b/_includes/themes/bootstrap-3/default.html @@ -19,7 +19,7 @@ - +